[ensembl-dev] Get Oligo probes

[njohnson]

Hi Sebastian

You probably want to have a look at our example script, found here:

	ensembl-funcgen/scripts/examples/microarray_annotation_example.pl

I will have a look at that error asap.

Thanks

Nathan Johnson

Ensembl Regulation
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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On 1 Apr 2014, at 08:50, Sébastien Moretti <sebastien.moretti at unil.ch> wrote:

> Hi
> 
> I wonder how to retrieve all gene_id and related probeset id for a given species and a particular chip type.
> Usually I get that from BioMart but cannot find the equivalent way of doing that with the Ensembl API
> e.g. Ensembl Gene ID 	Affy HG U95AV2 probeset
>     ENSG00000261657 	39195_s_at
>     ENSG00000234627 	37079_at
>     ENSG00000256305 	31325_at
>     ...
> 
> I tried the method fetch_all_by_linked_transcript_Gene but it fails with this error message:
> DBD::mysql::db selectcol_arrayref failed: Table 'homo_sapiens_core_75_37.transcript_stable_id' doesn't exist at /usr/local/ensembl/ensembl-funcgen/modules//Bio/EnsEMBL/Funcgen/DBSQL/BaseAdaptor.pm line 922.
> And the status of the method is "at risk".
> 
> 
> Any idea how to do that?
> Thanks
> 
> 
> 
> PS for the API documentation of fetch_all_by_linked_transcript_Gene() & fetch_all_by_linked_Transcript() a '}'  is missing at the end of the code example.
> 
> -- 
> Sébastien Moretti
> Department of Ecology and Evolution,
> Biophore, University of Lausanne,
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4221/4079
> http://selectome.unil.ch/ http://bgee.unil.ch/
> 
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